User: doctor.dee005
doctor.dee005 • 170
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- Bioinformatics Center, Pune
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- 1 day, 13 hours ago
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Posts by doctor.dee005
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... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there.
[1]: http://www.drive5.com/pop/VTML200I ...
written 5 days ago by
doctor.dee005 • 170
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... BLOSUM and PAM series matrices are available on NCBI ftp.
See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/ ...
written 7 days ago by
doctor.dee005 • 170
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... use this [Python script][1]. Easy to use: python contigPlot.py fastaDir.
Where fastaDir is directory name containing genome files (extension .fasta)
[1]: https://github.com/drdee255/code-Util/blob/master/contigPlot.py ...
written 7 days ago by
doctor.dee005 • 170
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... I have several microbial genomes and protein files from multiple genera. I have tried [BPGA][1] but it cantbe automated.
[1]: http://iicb.res.in/bpga/index.html ...
written 8 weeks ago by
doctor.dee005 • 170
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... I am doing pan genome analysis of multiple genera. I am searching a tool which will work on protein files (I have annotated proteins for each genome). I wanted to run [Roary][1], but it requires .gff files as well.
Any suggestions are welcomed.
[1]: https://github.com/sanger-pathogens/Roary/tre ...
written 8 weeks ago by
doctor.dee005 • 170
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... You can use efetch from ncbi-entrez-direct utilities. But first, you must have the accessions (with start and end of seuences which you want to extract). Make one file for this data and use following command in any script.
efetch -db nuccore -id NG_007524.1 -format fasta -chr_start start -chr_stop ...
written 9 weeks ago by
doctor.dee005 • 170
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... Use [seq_stat.py][1], it will give output as tab-separated file, containg header, count of each nucleotide and sequence length. If multifasta file is provided, it will print this statistics. The sequence length of each sequence will be in last column.
[1]: https://github.com/drdee255/Python-code ...
written 9 weeks ago by
doctor.dee005 • 170
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... use [fastq-pair][1], it gives the only reads which are in forward and reverse files. So, rather than making forward.txt(headers), make forward.fastq(containg reads for which you want reverse reads to be extracted) and run the program.
This will make four files in the directory:
1. forward.fastq.p ...
written 9 weeks ago by
doctor.dee005 • 170
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... The trailing unaligned regions are results of global alignments. Use mafft --localpair (local alignment), in which trailing unialign regions from both the ends are not considered in order to maximiza alignment scores. ...
written 10 weeks ago by
doctor.dee005 • 170
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... You can use [trimmomatic][1] for this kind of trimming where you can include your adapters in their adapter library and perform trimming.
[1]: http://www.usadellab.org/cms/?page=trimmomatic ...
written 10 weeks ago by
doctor.dee005 • 170
Latest awards to doctor.dee005
Teacher
5 days ago,
created an answer with at least 3 up-votes.
For A: Amino Acid matrices freely downloadable url
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Extract specific fasta sequences from multiple multi-fasta files located in a di
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